input:
  paths:
    - "~/Pictures"
    - "/mnt/storage3/aman/screenshots"
  patterns:
    - "SCR-*.png"
    - "*.jpg"
    - "*.jpeg"
    - "*.tiff"
    - "*.bmp"
  recursive: true

ocr:
  engine: "paddleocr"  # "paddleocr" | "tesseract" | "auto"
  languages: ["en"]  # For tesseract: eng, lat, deu, fra, spa, ita, por, chi_sim, jpn, kor
  use_gpu: false
  use_angle_cls: true
  det_db_thresh: 0.3
  det_db_box_thresh: 0.6
  det_db_unclip_ratio: 1.5
  rec_batch_num: 6
  cpu_threads: 4
  preprocess:
    deskew: true
    denoise: true
    clahe: true
    adaptive_threshold: true
    remove_lines: true
    max_dimension: 4096

processing:
  workers: 4
  batch_size: 10
  retry_attempts: 2
  timeout_per_image: 120
  skip_existing: true

detectors:
  figures:
    enabled: true
    model: "lp://PubLayNet/faster_rcnn_R_50_FPN_3x/config"
    confidence_threshold: 0.7
  tables:
    enabled: true
    model: "microsoft/table-transformer-detection"
    confidence_threshold: 0.7
  captions:
    enabled: true
    model: "lp://PubLayNet/faster_rcnn_R_50_FPN_3x/config"
    confidence_threshold: 0.5

entities:
  enabled: true
  model: "en_core_sci_lg"
  types:
    - "GENE"
    - "PROTEIN"
    - "CHEMICAL"
    - "SPECIES"
    - "DISEASE"
    - "CELL_LINE"
    - "ORGANISM"
    - "CELL_TYPE"
  merge_entities: true

citations:
  regex_enabled: true
  grobid_enabled: false
  grobid_url: "http://localhost:8070"
  grobid_timeout: 30

chunking:
  chunk_size: 1000
  chunk_overlap: 200
  separators: ["\n\n", "\n", ". ", " ", ""]
  keep_separator: true

output:
  base_directory: "./data/ocr_output"
  format: "markdown"
  organize_by: "date_run"  # "date_run" | "source_dir" | "flat"
  frontmatter:
    - "source_path"
    - "source_hash"
    - "timestamp"
    - "ocr_engine"
    - "ocr_confidence_mean"
    - "language"
    - "detected_entities"
    - "has_figures"
    - "has_tables"
    - "citations_found"
    - "chunk_index"
    - "total_chunks"

watch:
  enabled: true
  debounce_seconds: 5
  ignore_patterns:
    - ".DS_Store"
    - "*.tmp"
    - "*.partial"
    - "*.crdownload"
  db_path: "./data/processed_files.db"
  poll_interval: 1.0